The information provided herein and references cited are provided solely to assist the understanding of the reader, and does not constitute an admission that any of the references or information are prior art to the present invention.
With the explosion of techniques for the synthesis, analysis and manipulation of nucleic acids, numerous new opportunities have arisen in diagnostics and therapeutics. In research there is substantial interest in being able to identify DNA sequences, which may be associated with specific organisms, alleles, mutations, and the like, to understand particular genetic processes, to identify diseases, for forensic medicine, etc. Also, for many purposes, one may wish to modulate the expression of a target gene, so as to identify the function of such gene, or the cellular changes brought about by changes in the expression of such gene. In therapeutics, one may wish to inhibit the proliferation of cells, such as bacterial, fungal and chlamydia cells, which may act as pathogens, of viruses, of mammalian cells, where proliferation results in adverse effects on the host, or other situations. In vivo, one may provide for reversible or irreversible knock out, so that information can be generated on fetal development, or the effect on the organism of reduced levels of one or more genetic products.
Polyamide oligomers of nitrogen-containing five-membered heterocycles can be used to bind predetermined sequences on double stranded DNA (dsDNA). DNA recognition by polyamide oligomers depends on a code of side-by-side amino acid pairings that are oriented in the amino to carboxyl direction with respect to the 5′-3′ direction of the DNA helix. Thus, polyamide oligomers bind dsDNA in an antiparallel fashion and in a stoichiometric ratio of 1:2, oligomer to DNA (Dervan et al., “Sequence-Specific DNA Recognition by Polyamides,” Current Opinion in Chemical Biology, Vol. 3: 688, 1999). Antiparallel pairs of certain five-membered heterocycles preferentially bind to specific base pairs on duplex DNA. These antiparallel pairs have proven useful for the recognition of hundreds of predetermined DNA sequences by polyamide oligomers. Listed below in Table 1 are representative polyamide pairs of five-membered heterocycles and the DNA pairs that they preferentially bind to, referred to herein as the “pairing rules.”
TABLE 1Pairing Rules for Five-Membered HeterocylesPolyamideDNA base pairPair*recognitionIm/PyG·CPy/ImC·GHp/PyT·APy/HpA·T*Im = N-methyl imidazole; Py = N-methyl pyrrole; Hp = 3-hydroxypyrrole
The five-membered heterocycles described thus far in DNA-binding polyamide oligomers are analogues of the pyrrole ring. Their chemical design mimics the natural products netropsin and distamycin A, molecules which bind the minor groove of DNA (Arcamone, F. et al., “Structure and Synthesis of distamycin A, Nature, Vol. 203: 1064, 1964; Pelton, J. G. et al., “Structural characterization of a 2:1 distamycin-A-D(CGCAAATTGGC) (SEQ ID NO: 9) complex by two-dimensional NMR,” Proc Natl Acad Sci USA, Vol. 86: 5723-5727, 1989).
Efforts have been devoted to extend the ensemble of five-membered heterocycles that are capable of cooperatively pairing with each other to recognize specific DNA base pairs. These efforts have, in part, been motivated by the instability of the Hp heterocycle towards acids and free radicals. Polyamide oligomers containing Hp are susceptible to such degradation, and a robust replacement for use in biological applications is desired.
A search for new five-membered heterocycles and new five-membered heterocycle pairs for sequence determination was recently attempted with little success (Marques, M. et al., “Toward an Understanding of the Chemical Etiology for DNA Minor-Groove Recognition by Polyamides,” Helvetica Chimica Acta, Vol. 85: 4485-4517, 2002). Using molecular modeling from an X-ray crystallography structure of a polyamide oligomer bound to duplex DNA, analogs of the existing five-membered heterocycles were designed to optimize binding to the curvature and twist of minor-groove DNA. Analogs of Py (1-methyl-1H-pyrazole (Pz) and 1H-pyrrole (Nh)), Im (5-methylthiazole (Nt) and furan (Fr)), and Hp (3-hydroxythiopene (Ht)) were synthesized and investigated in polyamide pairs. Additional sulfur containing pyrrole analogs (4-methylthiazole (Th), 3-methylthiophene (Tn), and thiophene (Tp)) were also studied. The chemical structures of these analogs are shown below:

These eight analogs of the five-membered heterocycles Py, Im, and Hp and their corresponding pairs did not result in new sequence discrimination. These findings imply that DNA recognition by the existing pairs, namely Im/Py, Py/Im, Hp/Py, and Py/Hp, may be facilitated within a narrow structural window; thus, a search for new five-membered heterocycles may be of limited value.
Six-membered heterocycles represent a new class of heterocycles that may be employed in oligomers which bind DNA. Certain small molecule ligands known to bind the minor groove of DNA with relatively high affinities contain six-membered heterocycles and fused heterocycles, such as benzimidazole, imidazopyridines, and indoles (R. L. Lombardy, et al., J. Med. Chem., 39: 1452-1462, 1996; Minehan, T. G. et al. Helv. Chim. Acta, 83: 2197-2213, 2000; Wang, L. et al., Biochemistry, 40: 2511-2521, 2001; Zhang, W. et al., FEBS Lett., 509: 85-89, 2001; Ji, Y.-H. et al., Bioorg. Med. Chem., 9: 2905-2919, 2001; Satz, A. L. et al., J. Am. Chem. Soc., 123: 2469-2477, 2001; Behrens, C. et al., Bioconjugate Chem., 12: 1021-1027, 2001; Matsuba, Y. et al., Cancer Chemother. Pharmacol., Vol. 46: 1-9, 2000).
Hoechst 33258, which comprises a bis-benzimidazole, an N-methylpiperazine, and a phenol moiety, is an example of a fused six-membered cyclic derivative (P. E. Pjura, K. Grzeskowiak, R. E. Dickerson, J. Mol. Biol., 197: 257-271, 1987; M. Teng, N. Usman, C. A. Frederick, A. Wang, Nucleic Acids Res., 16: 2671-2690, 1988; S. Kumar, B. Yadagiri, J. Zimmermann, R. T. Pon, J. W. Lown, J. Biomol. Struct. Dyn., 8: 331-357, 1990). The chemical structure of Hoechst 33258 is shown below:
Hoechst 33258 is a highly fluorescent dye which binds the minor groove of DNA at A•T rich tracks. Oligomers of the Hoechst benzimidazoles have been synthesized and studied for DNA recognition (Minchan, T. G. et al., “Molecular Recognition of DNA by Hoechst Benzimidaoles: Exploring Beyond the Pyrroe-Imidazol-Hydroxypyrrole Polyamide-Pairing Code,” Helvetica Chimica Acta, Vol. 83: 2197-2213, 2000). These benzimidazole oligomers also show preference for A•T rich sequences, as well as for 5′-WGWWW-3′ and 5′-WCWWW-3′, where W=A or T.
While Hoechst 33258 and its corresponding benzimidazole oligomers bind A•T rich DNA in a 1:1 ratio, such compounds do not recognize specific nucleotide base pairs across the duplex, such as in the pairing rules described above for five-membered heterocyclic polyamide oligomers. Other six-membered heterocyclic DNA binding ligands reported thus far also do not recognize specific mononucleotide base pairs across the duplex.